statalign.postprocess.plugins
Class ConsensusNetwork

java.lang.Object
  statalign.postprocess.Postprocess
      statalign.postprocess.plugins.ConsensusNetwork

public class ConsensusNetwork
extends Postprocess

This is the postprocessmanager for showing the consensus network.

Author:

miklos, novak, wood

Field Summary

javax.swing.JPanel

pan

Fields inherited from class statalign.postprocess.Postprocess

active, alignmentType, file, hasToolBar, mcmc, outputable, outputFile, postprocessable, postprocessWrite, rnaAssociated, sampling, screenable, selected, show

Constructor Summary

ConsensusNetwork()
It construct a postprocess that is screenable (=can be shown on the GUI), outputable (= can be written into th elog file) but not postprocessable (= cannot generate its own output file).

Method Summary

void	afterLastSample() Empty function, since there is nothing to do after the last sample in this postprocess thread.
void	beforeFirstSample(InputData inputData) Initializes the graphical interface.
java.lang.String	getFileExtension() Returns default file extension that is to appended to the input file name to get the file this plugin is writing into.
javax.swing.Icon	getIcon() It generates a new icon based on the figure in file icons/calignment.gif
javax.swing.JPanel	getJPanel() It constructs a new JPanel, and returns with it
java.lang.String	getTabName() It returns with its tab name, 'Alignment'
double	getTabOrder() Specifies the order of the tab for this plugin in the GUI.
java.lang.String	getTip() It returns with the tip of the tabulated panel 'Current alignment in the Markov chain' (shown when mouse is moved over the panel)
void	newSample(State state, int no, int total) At each MCMC sampling point, the current alignment is shown on the GUI.
void	setSampling(boolean enabled) Toggles sampling mode.

Methods inherited from class statalign.postprocess.Postprocess

addTrack, getDependences, getModExtPlugins, getToolBarItems, getTracks, init, newPeek, newSample, newStep, refToDependences, reloadPanel, setSelected

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

pan

public javax.swing.JPanel pan

Constructor Detail

ConsensusNetwork

public ConsensusNetwork()

It construct a postprocess that is screenable (=can be shown on the GUI), outputable (= can be written into th elog file) but not postprocessable (= cannot generate its own output file).

Method Detail

getJPanel

public javax.swing.JPanel getJPanel()

It constructs a new JPanel, and returns with it

Specified by:

getJPanel in class Postprocess

Returns:

Returns with the panel of the GUI

getIcon

public javax.swing.Icon getIcon()

It generates a new icon based on the figure in file icons/calignment.gif

Specified by:

getIcon in class Postprocess

Returns:

Returns with the icon that will appear on the label of the tabulated panel.

getTabName

public java.lang.String getTabName()

It returns with its tab name, 'Alignment'

Specified by:

getTabName in class Postprocess

Returns:

Returns with the name that will appear on the label of the tabulated panel.

getTip

public java.lang.String getTip()

It returns with the tip of the tabulated panel 'Current alignment in the Markov chain' (shown when mouse is moved over the panel)

Specified by:

getTip in class Postprocess

getTabOrder

public double getTabOrder()

Description copied from class: Postprocess

Specifies the order of the tab for this plugin in the GUI.

E.g. we probably always want the "sequence input"-tab to appear first and therefore it returns a 1.0d here. The "current alignment"-tab returns 2.0d here and so if we want to make a tab get ordered between the "sequence input" and the "current alignment"-tabs we just make that plugin return 1.5d or something similar here. By default tabs get ordered last.

Overrides:

getTabOrder in class Postprocess

Returns:

the tab order of the tab associated with this plugin, if running in a GUI.

getFileExtension

public java.lang.String getFileExtension()

Description copied from class: Postprocess

Returns default file extension that is to appended to the input file name to get the file this plugin is writing into.

Overrides:

getFileExtension in class Postprocess

beforeFirstSample

public void beforeFirstSample(InputData inputData)

Initializes the graphical interface.

Overrides:

beforeFirstSample in class Postprocess

newSample

public void newSample(State state,
                      int no,
                      int total)

At each MCMC sampling point, the current alignment is shown on the GUI. Also, it writes the current alignment into the log file when in sampling mode.

Overrides:

newSample in class Postprocess

Parameters:

state - A State object representing the current state of the chain

no - The number of the current sample

total - The number of the total samples

setSampling

public void setSampling(boolean enabled)

Toggles sampling mode.

Specified by:

setSampling in class Postprocess

Parameters:

enabled - Set it true if you need samples.

afterLastSample

public void afterLastSample()

Empty function, since there is nothing to do after the last sample in this postprocess thread.

Overrides:

afterLastSample in class Postprocess